Contacts of the strand formed by residues 694 - 697 (chain C) in PDB entry 3UEO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 694 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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649C CYS* 3.4 18.7 - - - +
650C VAL 3.5 1.7 + - - +
651C ILE* 3.6 19.1 - - + -
652C SER 3.1 23.4 + - - -
679C PHE* 3.8 9.8 - - - -
692C SER* 3.8 0.8 - - - -
693C THR* 1.3 113.8 + - - +
695C LEU* 1.3 63.2 + - - +
696C ILE* 5.0 1.1 - - + -
714C PRO* 3.6 15.1 - - + +
716C VAL* 4.9 3.1 - - + -
720C TRP* 3.5 30.3 - + + -
730C ARG* 3.4 22.0 + - - -
733C GLU* 2.7 34.4 + - + +
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Residues in contact with LEU 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C SER* 3.8 19.1 - - - +
654C SER* 4.0 8.1 - - - -
679C PHE* 3.7 18.3 - - + -
694C HIS* 1.3 73.9 - - - +
696C ILE* 1.3 58.9 + - - +
697C LEU* 4.1 16.8 - - + -
704C LYS* 3.5 60.6 - - + +
705C TYR* 3.5 11.2 - - - +
708C ALA* 4.1 2.2 - - + -
714C PRO 2.8 9.3 + - - +
715C ALA* 3.9 20.6 - - + -
716C VAL* 2.7 36.2 + - - +
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Residues in contact with ILE 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651C ILE* 3.8 28.3 - - + -
652C SER 3.0 8.8 + - - +
653C PHE* 3.4 31.7 - - + -
654C SER 3.0 23.7 + - - +
656C CYS* 4.5 0.3 - - - -
694C HIS* 5.0 1.3 - - + -
695C LEU* 1.3 77.4 - - - +
697C LEU* 1.3 65.3 + - - +
716C VAL* 3.4 14.6 - - + -
717C THR 3.8 12.3 - - - +
718C ILE* 3.8 27.8 - - + -
720C TRP* 3.9 25.1 - - + -
721C LEU* 4.1 15.0 - - + -
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Residues in contact with LEU 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C SER* 3.4 24.0 - - - +
655C GLN* 3.5 11.2 - - - +
656C CYS* 4.9 1.6 - - - -
695C LEU* 4.1 15.7 - - + -
696C ILE* 1.3 76.1 - - - +
698C LYS* 1.3 66.9 + - - +
699C GLU 3.1 21.1 - - - +
705C TYR* 3.9 31.2 - - + -
715C ALA 4.2 4.7 - - - -
716C VAL 3.0 27.0 + - - +
717C THR* 3.6 13.9 - - - -
718C ILE* 3.8 9.5 + - - +
738C ILE* 3.5 29.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il